Use:
php index.php welcome show
as command in your crontab. E.g.:
0 * * * * php /home/username/index.php welcome show
Source (ver. 2.2.0)
http://www.codeigniter.com/userguide2/general/cli.html
Source (ver. 3.*)
http://www.codeigniter.com/user_guide/general/cli.html
Source (ver. 4.*)
http://codeigniter.com/user_guide/cli/cli.html